Contents    ◾    ix

Chapter 6    ◾    Chromatin Immunoprecipitation Sequencing

213

6.1 INTRODUCTION TO CHROMATIN IMMUNOPRECIPITATION

213

6.2 CHIP SEQUENCING

214

6.3 CHIP-SEQ ANALYSIS WORKFLOW

215

6.3.1

Downloading the Raw Data

217

6.3.2

Quality Control

218

6.3.3

ChIP-Seq and Input Read Mapping

219

6.3.4

ChIP-Seq Peak Calling with MACS3

223

6.3.5

Visualizing ChIP-Seq Enrichment in Genome Browser

226

6.3.6

Visualizing Peaks Distribution

229

6.3.6.1 ChIP-Seq Peaks’ Coverage Plot

230

6.3.6.2 Distribution of Peaks in Transcription Start Site (TSS)

Regions

233

6.3.6.3 Profile of Peaks along Gene Regions

234

6.3.7

Peak Annotation

235

6.3.7.1 Writing Annotations to Files

237

6.3.8

ChIP-Seq Functional Analysis

239

6.3.9

Motif Discovery

243

6.4 SUMMARY

250

REFERENCES

251

Chapter 7    ◾    Targeted Gene Metagenomic Data Analysis

253

7.1. INTRODUCTION TO METAGENOMICS

253

7.2 ANALYSIS WORKFLOW

254

7.2.1

Raw Data Preprocessing

254

7.2.2

Metagenomic Features

255

7.2.2.1 Clustering

255

7.2.2.2 Denoising

256

7.2.3

Taxonomy Assignment

258

7.2.3.1 Basic Local Alignment Search Tool

258

7.2.3.2 VSEARCH

259

7.2.3.3 Ribosomal Database Project

259

7.2.4

Construction of Phylogenetic Trees

260

7.2.5

Microbial Diversity Analysis

261

7.2.5.1 Alpha Diversity Indices

262

7.2.5.2 Beta Diversity

262